Sherrill et al, 2014
RNA sequencing was performed to quantify transcripts present in esophageal biopsy specimens obtained from 6 healthy controls (Control) and 10 patients with active EoE (EoE).
Rochman et al, 2014
TE-7 cells (a human esophageal epithelial cell line) were stimulated with IL-13 (100 ng/ml) for 2h, 6h, or 24h. Transcript levels were quantified by RNA sequencing. Untreated cells (Control_2h, Control_4h, Control_24h); IL-13-treated cells (IL-13_2h, IL-13_6h, IL-13_24h).
Azouz et al, 2018
A telomerase-immortalized human esophageal epithelial cell line (EPC2 cells) was transfected with either non-silencing control shRNA or SPINK7 shRNA. Cells were grown either in monolayer culture (undifferentiated) or in air liquid interface (ALI) cultures (differentiated). Transcript levels of the following types of cells were determined: cells transfected with non-silencing control shRNA and grown in monolayer culture (Undif_NSC); cells transfected with non-silencing control shRNA grown at the ALI (NSC); cells transfected with SPINK7 shRNA grown at the ALI (SPINK7_silenced).
Sherrill et al, 2014
A telomerase-immortalized human esophageal epithelial cell line (EPC2 cells) was grown submerged in monolayer culture (undifferentiated) for 8 days, or were grown submerged in monolayer culture for 8 days followed by 6 days of culture at the air liquid interface (differentiated). In some cases, cells were treated with IL-13 (100 ng/ml) during the 6 days of ALI culture. Transcript levels of the following conditions were assessed by RNA sequencing: Day_0: cells grown submerged for 8 days; Day_6: cells grown submerged for 8 days and then grown at the ALI for 6 additional days; Day_6_IL-13: cells grown submerged for 8 days and then grown at the ALI for 6 additional days in the presence of IL-13.
Blanchard et al, 2006
Blanchard et al, 2007
Caldwell et al, 2010
RNA isolated from distal esophageal tissue was subjected to genome-wide transcript profile microarray analysis. Experimental groups: NL: control; CE: chronic esophagitis; EoE: active EoE; EoE+FP+R: fluticasone responder; EoE+FP+NR: fluticasone non-responder.
Blanchard et al, 2007
RNA isolated from gastric antrum tissue was subjected to genome-wide transcript analysis by microarray analysis. Experimental groups: control and active eosinophilic gastritis (EoG).
Caldwell et al, 2014
Human primary esophageal epithelial cells from patients with EoE were cultured in the presence or absence of IL-13 (100 ng/ml) for 48 h, and the mRNA was subjected to genome-wide transcript profile microarray analysis. The data from the IL-13-stimulated cells were normalized pairwise to unstimulated controls.
Shoda et al, 2018
RNA was isolated from distal esophageal tissue of 86 individuals with active EoE. The RNA was subjected to EDP analysis, which quantifies 96 individual gene transcripts. Graphs depict the -deltaCt value -(ct of GAPDH – ct of gene of interest) for each individual. Experimental groups: EoEe1: EoE endotype 1; EoEe2: EoE endotype 2; EoEe3: EoE endotype 3.
Wen et al, 2019
Single-cell transcriptome profililng of esophagus biopsies from patients with active eosinophilic esophagitis (EoE, n=11), in remission (n=6), and without disease (n=5).
Ben Baruch-Morgenstern et al, 2016
17 samples were analyzed in this experiment. The experiment was designed with 3 replicates for each treatment/genotype/tissue (Dox and no Dox/wildtype and knockout/bone marrow and esophagus), with the exception of the sample wildtype bone marrow no Dox where 1 replicate was dropped due to low hybridization signal. The no Dox and wildtype samples are controls for the treatment and background of the mice. Experimental groups: bm_WT_noDox: bone marrow, wildtype, no Dox; bm_KO_noDox: bone marrow, PirB knockout, no Dox; bm_WT_Dox: bone marrow, wildtype, Dox; bm_KO_Dox: bone marrow, PirB knockout, Dox; eso_WT_Dox: esophagus, wildtype, Dox; eso_KO_Dox: esophagus, PirB knockout, Dox.
Shoda et al., 2022
RNA sequencing was performed to quantify transcripts present in colon biopsy specimens obtained from 8 control individuals (Non_EoC) and 6 patients with active EoC (Active_EoC).
Shoda et al, 2020
RNA sequencing was performed to quantify transcripts present in gastric biopsy specimens obtained from 12 healthy controls (Non-EoG) and 9 patients with EG (EoG).
Bouffi et al, 2013
RNA sequencing was performed to quantify transcripts present in LDBM Mouse Eosinophils untreated, treated with IL-4, or treated with IL-33 at 1 hour and 4 hours.
Rochman et al, 2020
For the monolayer cultures, EPC2 cells were seeded at a density of 2.5x10^5 cells/well in KSFM in a 24-well plate. The next day, the medium was replenished. After 24 hours, stimulants were added in a total of 350 to 500mL of fresh medium for 24 hours. IL-13 was added to a final concentration of 100 ng/mL unless otherwise indicated. Omeprazole and esomeprazole were dissolved in DMSO to the stock concentration of 100 mM, aliquoted into 10-mL amounts, and stored at –80°C. PPIs were thawed once and used at a working concentration of 100mM; cells were pretreated with the PPIs for 1 hour before adding IL-13 to the medium. GNF-351 was dissolved in DMSO to a 20 mM stock concentration. The stock was aliquoted in 10-mL doses and stored at –80°C. Cells were pretreated with GNF-351 at a final concentration of 2mM for 30 minutes before adding PPIs.
RNA sequencing was performed with high-quality RNA (RNA integrity number > 8) by using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, Vienna, Austria, catalog no 015.96).
Libraries were diluted to final concentrations of 5 nM and sequenced on a HiSeq 4000 Illumina sequencing machine at the Genomics and Cell Characterization Core Facility at the University of Oregon with 100- to 150-bp-length single reads.
Multiplex analysis was performed by Eve Technologies (Calgary, Canada) using the Human Cytokine Array/Chemokine Array 65-Plex Panel (HD65).
Brusilovsky et al, 2022
The contribution of vitamin D (VD) deficiency to the pathogenesis of allergic diseases remains elusive. We aimed to define the impact of VD on esophageal allergic inflammation. To this end, we examined the potential clinical relevance of the esophageal epithelial cell (EPC2) transcriptional responses to IL- 13 or VD. Cells were grown in the monolayer culture at a super-confluent state (1×106 cells/cm2). Cells were treated with recombinant human IL- 13 (100 ng/ mL) and/or VD (1,25- dihydroxycholecalciferol; 100 nM) and subjected to bulk RNA sequencing.
Zuo et al. 2010, JI
Bi-transgenic mice (CC10-iIL-13) were generated in which IL-13 was expressed in a lung-specific manner that allowed for external regulation of the transgene expression, as previously described(13).
RNA from the esophagus or lung of IL-13 inducible transgenic mice obtained after 30 days of DOX or NO-DOX treatment was subjected to gene chip analysis using MOE 430 2.0 chips as previously reported (15). Gene transcript levels were determined using algorithms in the Microarray Analysis Suite and GeneSpring software (Silicon Genetics). For comparison with human EoE, genes were translated to human homologues represented on the human U133 chip using GeneSpring software and compared to microarray results previously described(8, 15). Welch T test and fold change cut-off were performed. The correlation between IL-13 expression and numbers of dysregulated genes were also analyzed using GeneSpring software.
2 NO-DOX samples and 3 DOX samples
MOE 430 2.0 chips - Affymetrix
Composition of probe sets can be identified/analyzed on NetAffx
RNA sequencing was performed to quantify transcripts present in duodenal biopsy specimens obtained from non-EoD controls (NL), patients with duodenal eosinophilia (DE), or patients with eosinophilic duodenitis (EoD). Graphs were depicted by the TPM for each individual.
Ben-Baruch Morgenstern et al. 2022, JACI
Rochman et al. 2022, JCI
Esophageal biopsies were obtained from patients with active EoE (n = 5), patients with EoE in histologic remission (n = 3), and control individuals with histologically normal esophageal biopsies and no history of esophageal disease (n = 2) and were subjected to 10X scRNA-sequencing.
Esophageal biopsies were obtained from patients with active EoE (n = 5), patients with EoE in histologic remission (n = 3), and control individuals with histologically normal esophageal biopsies and no history of esophageal disease (n = 2) and were subjected to 10X scRNA-sequencing. This dataset includes mast cells only.
Rochman et al. 2022, JCI
Esophageal biopsies were obtained from patients with active EoE (n = 5), patients with EoE in histologic remission (n = 3), and control individuals with histologically normal esophageal biopsies and no history of esophageal disease (n = 2) and were subjected to 10X scRNA-sequencing. This dataset includes epithelial cells only.